Hi Justin, That sounds perfect to me. I think using the water.mdp file and water.top file I can create my own water.gro file including any number of molecules i guess.
I realized one more thing that I need to create my own protein.ssd file from do_dssp program I guess, because in the tutorial I was given these files already but for my own protein I have to create one. In the MARTINI tutorial they have provided me the seq2itp.pl script which can convert my 1K4C.seq file to 1K4C.itp file but for that I need 1K4C.ssd file. The command is as: seq2itp.pl 1K4C.seq 1K4C.ssd > 1K4C.itp I don't know how to create 1K4C.ssd file now because when I try to create it using do_dssp it asks me to generate the topol.tpr file and I cannot generate that before simulation. Do you have any idea about this? Sunny On Mon, Aug 10, 2009 at 6:31 PM, Justin A. Lemkul<jalem...@vt.edu> wrote: > > > sunny mishra wrote: >> >> Hi Justin, >> >> Thanks for the expedient reply. In the MARTINI tutorial they have >> provided two water.gro files one for lipids and the other for >> proteins. Protein water molecule file consists of 10800 atoms of water >> and the lipid has 400 atoms. So even if I simulate any protein >> structure after converting that to CG, can I use the same water.gro >> file for protein always? >> > > I don't know about different water files based on the system; that seems a > bit arbitrary. I'm referring to the one single water.gro file here: > > http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html > > If there are differences between using the water structure with proteins and > lipids, any changes are likely reflected in the force field, version 2.0 for > lipids, and version 2.1, which is the extension to proteins, if there is a > difference at all. Any reasonable equilibrated box of water will probably > suffice; your equilibration will likely take care of any differences, if > they exist. > > -Justin > >> Sunny >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
